combineNet2target_list — combineNet2target

This function will create a combined target list of seed-partner driver pairs.

Usage

combineNet2target_list(
  target_list = NULL,
  seed_name = NULL,
  partner_name = NULL,
  return_type = "SINBA_originalID"
)

Arguments

target_list: list, the driver-to-target list object.target_list is generated by get.combined.network and contains all the driver gene regulons.
seed_name: the driver genes will be used as seed for combination, must be included the the target_list
partner_name: optional, the partner driver genes will be used as partner for combination. The default setting will use all the other drivers except the seed gene in the target_list.
return_type: character,the type of return data. User can choose from "SINBA_target_list" and "SINBA_originalID". Default is "SINBA_originalID", which returns the combination originalID name for downstream activity calculation, "SINBA_target_list" returns the full combination target list.

Examples

out_net_file1<-"path1_to_network_file/consensus_network_ncol_.txt"
out_net_file2<-"path2_to_network_file/consensus_network_ncol_.txt"
net1  <- get.single.network(network_file=out_net_file1)
#> Error in get.single.network(network_file = out_net_file1): could not find function "get.single.network"
net2  <- get.single.network(network_file=out_net_file2)
#> Error in get.single.network(network_file = out_net_file2): could not find function "get.single.network"
combined.network<-get.combined.network(network1=net1,network2=net2)
#> Error in get.combined.network(network1 = net1, network2 = net2): could not find function "get.combined.network"
sinba_target_list<-combineNet2target_list(target_list=combined.network$target_list,seed_name="LCK")
#> Error in combineNet2target_list(target_list = combined.network$target_list,     seed_name = "LCK"): could not find function "combineNet2target_list"
sinba_target_list<-combineNet2target_list(target_list=SINBA.par$combined.network$target_list,seed_name="LCK",partner_name=c("BCL2","FYN"),return_type="SINBA_target_list")
#> Error in combineNet2target_list(target_list = SINBA.par$combined.network$target_list,     seed_name = "LCK", partner_name = c("BCL2", "FYN"), return_type = "SINBA_target_list"): could not find function "combineNet2target_list"
sinba_originalID<-combineNet2target_list(target_list=SINBA.par$combined.network$target_list,seed_name="LCK",partner_name=c("BCL2","FYN"),return_type="SINBA_originalID")
#> Error in combineNet2target_list(target_list = SINBA.par$combined.network$target_list,     seed_name = "LCK", partner_name = c("BCL2", "FYN"), return_type = "SINBA_originalID"): could not find function "combineNet2target_list"
if (FALSE) { # \dontrun{
} # }